The move is thought to be the first instance of a major partnership between an online and a bricks and mortar Christian retailer.
cbanews.org said the move will "save both companies time and money, and increase the reach of both their ministries".
The move, which was first announced in March, sees Eden and CLC both operating out of a property in Sandycroft, Wales. CLC owns the building and is leasing part of it to Eden.co.uk. The front of the distribution warehouse has signage from both companies.
CLC's Eddie Olliffe told cbanews the deal will benefit everyone: "I've always been troubled by the degree of antipathy that seems to exist between online and bricks-and-mortar stores, because it seems to negate the whole purpose of what we're here as Christians to do in terms of distributing Christian material. It doesn't really matter how that distribution takes place ... the important thing is that the distribution happens".
He said it would be "duplication of the worst type" if CLC attempted to compete with Eden.co.uk.
"My decision was that we would seek partnership wherever possible, so last September (2014) we asked Gareth Mulholland, managing director of Eden.co.uk whether he would fulfil our CLC UK online shop. So Eden.co.uk actually runs CLCbookshops.com; that's where our relationship started."
Mulholland told cbanews.org, "We thought we would be better off working together, particularly if we could be under one roof in one building...We're able to work more closely with one of our most significant suppliers...We have different focuses, but we'll benefit from working together."